arrival flight # ?: JFK New York or Taipei (connecting flight) for China visa free transit.

Actually, this is fairly simple. The first thing is to have a clear presentation of your flight and cruise itinerary. If I am not wrong, your itinerary is:

Taipei - Shanghai - Japan
Japan - Shanghai - US

Now, the most important question is, do you have any additional stops in some country or territory between those points. I assume you might have a stop between Shanghai and US if you use Eva Air flights because there is no direct flight, operated by Eva Air, between Shanghai and US. It should be again via Taipei.

So, if your immediate points before and after Shanghai are exactly like this:

Taipei - Shanghai - Japan
Japan - Shanghai - Taipei

Then you are definitely and undeniably eligible for 144 hour visa free transit in Shanghai twice.

You should always remember that you will travel via Shanghai using 144 hour visa free transit and you should have your flight and cruise tickets at hand. It would be ideally to print them out to speed up the entire procedure.

So, upon your landing in Pudong airport, the first thing is to approach 24/144 hour visa free transit counter where you will apply for a temporary entry permit in order to be allowed to exit the airport. You will present your flight and cruise tickets and that is all. This application is a formality and is free of any charge. After a short check, you will be granted a permit and you will head to immigration and formally enter China in order to enjoy your free time until the time of your cruise departure arrives.

After your arrival from Japan, you will perform the same procedure at the Shanghai (Wusongkou) cruise port as you have done at the airport upon your first arrival in China and that's it. You will spend an overnight in Shanghai and then proceed to catch your flight to Taipei and then from there toward US.